Ten structural genes from the Capsicum (pepper) carotenoid biosynthetic pathway have been localized on a (Capsicum annuum x Capsicum chinense)F-2 genetic map anchored in Lycopersicon (tomato). The positions of these genes were compared with positions of the same genes in tomato when known, and with loci from pepper, potato, and tomato that affect carotenoid levels in different tissues. C2, one of three phenotypically defined loci determining pepper fruit color, cosegregated with phytoene synthase, The capsanthin-capsorubin synthase (Ccs) locus, shown previously to cosegregate with Y, another pepper fruit color locus, mapped to pepper chromosome 6, Other structural genes in pepper corresponded to loci affecting carotenoid production as follows: Ccs in pepper and the a locus for hyperaccumulation of beta-carotene in tomato fruit mapped to homeologous regions; the position of the lycopene beta-cyclase gene in pepper may correspond to the lutescent-2 mutation in tomato; and the lycopene epsilon-cyclase locus in pepper corresponded to the lycopene epsilon-cyclase locus/Del mutation for hyperaccumulation of delta-carotene in tomato fruit. Additional associations were seen between the structural genes and previously mapped loci controlling quantitative variation in pepper and tomato fruit color. These results demonstrate that comparative analyses using candidate genes may be used to link specific metabolic phenotypes and loci that affect these phenotypes in related species.